Genetic, Structural, Physicochemical, and Molecular Epidemiological Landscape of Three New Mutations Found in the Spike (S) Protein of Highly Transmissible Sri Lankan Delta Variant Sub-lineage AY.28: A222V, A701S, and A1078S

Recently, three new mutations were identified in Sri Lanka the spike protein of rapidly spreading delta variant SARS-CoV-2 virus by sublineage AY.28. They A222V, A701S, and A1078S. The primary focus here is on A701S mutation that (1) found immediate vicinity S1/S2 cleavage site (PRRAR ∗ SV) separates S1 S2 subunits protein; (2) has high structural disorder region spanning Serine-701 (Ser-701), which promotes a longer flexible loop forming better substrate; (3) collapses loose, short, unstable, tripeptide beta strand (ENS), likely to assist host proteases cleave S1-S2 interface easily than when an alanine present. same at least 10 other strains India, USA (East West Coasts), China, classifies this as geographically widespread convergent etiology. Conversely, A1078S highly present (>60 strains) terms coronaviruses, while abundant A222V inferred genetic code, topological features, placement (in strand) be innocuous, conservative mutation. critical nature S1/S2-dependent makes one significance not just for possible higher transmission but also subsequent fates such viral load vaccine effectivity against variant.